I thought I'd add a second answer based on a separate incident today that I believe is relevant to the thought process behind this question.
@Anna/@xxx posted a question that some site members started to workshop. She'd spent a lot of time on that question and found that upsetting. She went and made a meta post and got a long explanation from another user. This upset the user to the degree that she initated the process of self-deletion.
Now, I want to say that all the site members involved were a) not being rude, they were polite and b) were largely correct in their critiques. They did not do anything "wrong" per se. However, the upset of the user involved is not "wrong" either. How can this be and what can we do about it?
Well, on SE we tend to take a very legalistic view of things. But real people have emotions, and so when a comment/answer/activity is correct but makes someone upset, we can't just hide behind "Well but we didn't mean to upset them it's all their problem," I think it's safe to say that general real-world thinking on inclusivity and interpersonal relations sees that as negligent. I think we could perhaps add more empathy, or EQ if you will, to our activities. (also see Crucial Conversations, How To Say It, How To Win Friends and Influence People, and other fine works along these lines)
After conducting some retrospectives with some site users in chat, I have constructed some possible changes I think could help with perceived rudeness. (We occasionally have real rudeness, which I address in my other answer, but I think in the juncture between community moderation and people's emotions, we have a separate problem of perceived rudeness.)
Understand when someone is upset and apply the same behavior you should in the real world. Here's a good, simply explained example: How To Handle People That Are Angry With You. (replace "you" with "the site and the other folks on it" if you're not one of the initial principals). When someone is upset, an immediate extended legal brief on their question's flaws and advice on how to fix it is, actually, not all that useful. I know that the SE rationalist way says that's totally the best solution, but we should probably have better awareness of context clues that someone is upset and not in lawyer mode right now. If someone's clearly venting on Meta, you can let it sit a little, respond with active listening and validation instead of a "fix," etc.
Find some ways for people to reach out and get additional help when they're having a problem. We allegedly have these, but they're kind of opaque to newer site users. How do you reach out to a mod? Well... You could ping in chat, if you go to chat and if you actually know the mods' names. You could post on meta and they will happen by eventually, probably. You could flag something, though in cases like this it's hard to understand which noun (comment etc.) to flag. We don't have a "contact the mods!" button or anything, maybe we should. I may propose that on meta.SE.
Find ways for people to get more help when they're having a problem. We have meta, which you already have to be a site ninja to go elicit wisdom from. We have the help center, which even though it gets popped up and linked a lot to new users, tends to be ignored. I can easily envision more contextual help, though. Your answer just got put on hold? Here's a notification to the "what does getting put on hold" mean part of the HC or meta Q or whatever. That could add context to help people understand that a random pogrom didn't just break out on them, but that there's some site dynamic going on.
I'd love to hear other suggestions of how we add more empathy to site operations.